A New Life
by C.W. Smith
Summary: An incident at Nerv leaves Shinji and Asuka in an unexpected predicament. Based on the original Idea of Claus von Stauffenberg, this is the "LD edition."
1. Change May I Borrow Your Skirt?

A New Life

"LD Edition"

Chapter 1: Change / Can I Borrow Your Skirt?

By: Lord Deathscythe

Disclaimer: I do not own Eva, that Anno guy does. I don't even own the original idea behind this story, that's Claus's. I do how ever want to try my take of that story and see what I can do with the… situation.

A shrine you could call it, looking over the small apartment. A shrine to memories good and bad, old and new. Pictures of a redheaded girl and a boy with dark blue eyes sharing a life time together decorated the shelves of this domain. In the kitchen of this place one man called home, Shinji Ikari prepared some food and drinks for two. Yui would be coming over today, spending time with her father while she prepared for the arrival of her own child.

Shinji was so happy that she had been able to grow up without having to worry about angel attacks or dying inside the cold entry plug of an Evangelion as he had. 

Although, her birth into this world was not without some pain on his part. A pain that he would relive time and again to see her smiling face as an infant.

He was so wrapped in memories of that time that he didn't notice that his daughter, Yui Suzahara, was watching him from the door.

"You know dad, if you're not careful you'll set the place on fire," Yui said with a smile.

"Or I'm just getting old. I was just thinking about when you were born. Now I get to see you have my grandchild." Shinji said as he smiled and greeted his daughter with a light hug. Yui was six months into her first pregnancy, and her belly had swelled with the growing life inside her. 

Shinji remembered the feeling well.

"Stop it dad. You are not that old you know. I mean, you and mom had me when you were still fifteen."

"Doesn't change the fact that I'm very happy for you. How's Keitaro doing?"

Since Yui had married Keitaro Suzahara two years ago, Shinji and Touji would sit down over a glass or two of sake and reminisce over when they had been kids. Of when they had been born, and talking of the time when they were made grandfathers themselves. Granted, Keitaro was a few years younger then Yui, but that didn't change the fact that they were in love. Touji and Shinji never really saw a problem with it. 

"He's doing fine dad. He's busy trying to get the rehabilitation center more funding and asked me if you might be interested in helping out. I mean, we both know how you feel about talking about what happened during the war, but it would help us get the money to keep things going."

Shinji shook his head with a wry grin on his face. "You know there are four things I could never say no to. Your mother, you, your sister, and a good cause."

Yui smiled at her father, and settled into a chair near the table.

Ever since Yui's mother had died a few years ago in the crash, her father had tried to continue on as well as he could. There were days Yui worried about him, thought he might be too wrapped in the past. He was only forty years old, and he had several good years left. Yui worried that being alone for so much time was bad for her father. She wouldn't be so worried if her father at least went out some. 

Not that she wanted him to go dating. Yui knew how much her father had loved her mother, and even after her being gone for three years she knew that he would never love someone the way he had mom. But it wouldn't hurt him to find a new friend or go out more often with Touji and Hikari. 

But that was dad, he was perfectly happy with things the way they were. Of course, if he didn't take his lithium as he should he'd get depressed.

Those times he had forgotten to take it had scared the hell out of Yui.

"So, how are you and the baby doing?"

"We're okay dad. I swear he's going to be a soccer player the way he kicks me."

Raising Yui was, to him, the single greatest achievement in his life. At one point, he gave that distinction to Eva; during a bittersweet period of his existence. But after living through the anguish that Eva brought, he wanted more than anything to put it past him. Even if he was a supposed savior of mankind. Now all these years later, Shinji Ikari did just that; his mind, heart, and soul focused only on the daughters in which he himself had a hand bringing into the world: His daughter.

And Asuka's.

In hindsight however, knowing what he knew now Shinji would gladly get back into Unit-01 if it meant he got to hold her and her sister when they were young. This soul, this person with eyes a shade of blue which was a perfect mixture of the blue in his and Asuka's eyes, was so important to him. 

Her sister, Misato, had been born when he and Asuka were a bit older. Shinji could see so much of Asuka in his youngest daughter; the fire and determination were all there. Yui took more after her father though, calm and reserved. The bond between father and daughter was strongest between Yui and Shinji

Considering how she had come into this world, there was little question as to why by those who knew. Not even Yui knew the whole truth about it. Perhaps now was the time to tell her about it. Now that she would be a parent herself he could tell her one of the biggest secrets he had. One that only he and a few others knew.

"Yui, you know about what happened the day you were born but there's a lot we never told you."

"Dad, I know that. It's not like everything was let out even after Nerv was dissolved."

"Yui, this is something that we kept secret for the simple reason that none of us knew how to explain it. Your uncles Touji and Kensuke, Aunt Hikari, Misato, even Asuka and myself didn't know how to tell you and we're the ones it happened to. I suppose the best way to start off is to show you something."

Shinji got up and moved to the living room. He grabbed one of the portraits of him and Asuka at fifteen then went to his room and pulled out an old shoe box from the top shelf of his closet. He settled back down into his chair and handed Yui the framed picture. This one happened to be one of Yui's favorites to look at. After so much pain and conflict to see her parents able to put it behind them like they had gave her a great sense of hope, no matter what was going on in her life.

Shinji opened the box and looked inside, a box full of pictures that hadn't been seen in a long time. His collection of memories he didn't want to share, but could never bring himself to forget. Photographs of bittersweet times in his life before he had really begun living, of when he had lived a reality of nightmares. He pulled one picture out of the box and handed it to Yui. 

Yui's eyes widened when she saw a young woman, resembling her father, in what she guessed to be her six month of pregnancy as well. The look on the girls face was one of sadness, loss. A look Yui could see in familiar dark blue eyes, and had seen on occasion.

When ever Shinji was sad himself, he had the exact same look.

Shinji then handed her another photo, this time of a young man with long red hair and eyes a lighter shade of blue. The features were all there, the eyes, the smirk, all looks she associated with her mother.

"What… what are these?"

"Pictures of something that happened to your mother and I while we were with Nerv. It was something we never really knew how we could explain it to anyone."

"Who are these two? I know you and mom were only children."

"They are us. It's a long and peculiar story Yui. I suppose I should start from the beginning. It happened about three months after the Eleventh Angel had attacked the Magi, and Ritsuko had devised a new experiment for us to be her guinea pigs in…"

--

Shinji and Asuka were feeling a bit uneasy after being briefed on the experiment Dr. Akagi had planned for today. To say it sounded more like science fiction then science fact would have been more accurate. Problem was when your job involved large robots and large monsters and you in said robots killing said monsters, these things weren't as spectacular as they would be to normal people. But still, this did seem a bit out there even for the good doctor.

"So you're going to fill the plugs up with these… robots and expect us to just sit there?" Asuka asked. It was a proven fact to Shinji that her accent went the opposite way of her patience, so the angrier she got the more you could here it. Right now he rated her at slightly put off by the idea just from the sound of her German heritage. Not to say he was completely comfortable with the idea either.

"Not robots per say Asuka. These are nanites. They are small enough to enter individual cells and make changes. The technology has been in development for years, but the data we collected from the eleventh angel helped bring it along to this point. This batch of Nanites has been programmed to go in and make minute repairs to your cells. If one cell is cancerous for example, the nanites will repair the cell. If anything you should feel much better when you get out of the plug then when you get in." explained the Ritsuko.

"Could something go wrong? I mean, what if they backfire?" asked a more then nervous Shinji.

"Don't worry, we will be monitoring them as they progress. If anything does happen, we can self destruct them before too much damage can be caused."

"Self-destruct?" No one in the room was happy with what that implied.

"Simply put, the nanites will shut down and dissolve into your system. No physical damage will occur because of that fail-safe."

This did little to settle Shinji and Asuka's stomachs.

--

While Shinji and Asuka prepared themselves in their entry plugs, preparations were made for the experiment. The test plugs had been modified so that a flow of the nanites could be feed into the plugs directly. Since both batches had been specifically programmed for their intended recipients, extreme care was give to make sure that was how it was set up. However, certain people had other plans for the Second and Third children. 

Unseen, a technician began altering the pump flow. He wasn't aware of what the reason for this was, but had learned not to question orders from his employer. Not to say that he wasn't curious, but what good or bad would come from this simple switch he was not told. He'd find out when everyone else did.

--

In the Pribnow Box, Ritsuko was checking the final preparations for the experiment. If all went well, then not only would they be able to shorten the pilots recovery time after missions but they would have proven the worth of nano-technology. Something that scientists had been trying to do for decades. Ritsuko was looking forward to this experiment more then most Nerv conducted. This test, unlike most of the experiments Nerv ran, was not top secret due to the nature of the technology used. If it was a success, then she had something to look forward to outside of Nerv circles. However, she doubted that with Commander Ikari's or Seele's scenarios she'd ever get the chance to enjoy that success.

"So, ready to make history Ritsu?" said the ever smooth voice of Ryoji Kaji.

"Everything we do here makes history Kaji. This is simply something that will make history and actually be recorded as history. Why are you here? I thought tests like this would bore you to death."

"I may not show it, but I do find what you do fascinating. And I have been interested in this little line of science on and off for years. I'd be a fool to miss such an opportunity."

"Just make sure you and Misato don't disturb the test. Okay?"

"Of course oh fair one of the test tubes."

With that Kaji moved to the side, watching the children as they were moved into the test plugs. He noticed something though he thought a bit… odd.

"Ritsu, why is Rei not taking part in this?"

"We were only able to produce enough nanites for two subjects. It was determined that Shinji and Asuka could benefit from the experiment the most so Rei will simply observe."

_That and Ikari ordered that in no way was Rei to be exposed to these nanites._ Ritsuko thought to herself, a bit more resentful of Commander Ikari's protectiveness of the First Child then normal. 

Final preparations were being made for the experiment. No one noticed the change on the flow from the storage tanks, or bothered to check the connections. 

--

Shinji and Asuka were secured in the test plugs, and all sensors had been activated to record data for the MAGI. As Misato entered the box, the final preparations had been made. 

"You sure this is safe Ritsuko? I don't like the idea of things screwing with their DNA."

"Everything is perfectly safe. I promise that when they come out they will be in much better health then when they went in. I guarantee it."

Ritsuko would soon be proven wrong.

"Ready to proceed Dr. Akagi," came the voice of Ritsuko's assistant. Maya worked diligently at her console, monitoring the experiment and making sure the MAGI received all the data for analysis.

"Good. Shinji, Asuka, we'll be starting the injection of the nanites now. If you feel tired all of the sudden don't worry. The nanites are programmed to put your bodies into a state of relaxation to aide in the repairs they'll be making. As soon as this test is completed you'll be moved to the infirmary until you regain consciousness."

"Yes ma'am." Came the unenthusiastic reply of the two Children turned guinea pigs.

"Maya start the flow at eight hundred thousand parts per million."

"Yes ma'am."

The LCL in the entry plugs began to darken as millions of the microscopic droids began to pour in. As Shinji and Asuka hesitantly inhaled the constructs they began to tire due to the sedating effects of the nanites. As they went into a deep slumber, the nanites began the work of doing repairs to their hosts. But as they did the nanites noticed something extremely off about their individual hosts cells. The nanites in Shinji had been programmed to make alterations and repairs based on a female's physiology. That the host had a chromosome off gave the nanites cause to think for a moment. Why would the genes of their host be in a male configuration and not female? The answers to the nanites were blatantly simple, change the offending chromosome and then make sure the rest of the body was the way it should be. 

The nanites that had begun work inside Asuka's body had come to the same relative conclusion.

So, the nanites began to alter each and every cell in Shinji and Asuka's bodies to fit with what they were expecting. As the nanites determined that certain characteristics in their hosts were either missing or over developed they made changes as well. The production of certain hormones and chemicals in both children was increased or decreased to aide in bringing the host body to the developmental point they should be at. Where there was too much tissue, the nanites digested it and then used that material to fashion the missing organs that each host required. 

As the nanites didn't consider this an error in their program, it went completely unnoticed by the main computer. The one person who noticed the abnormality was Rei.

She had been observing Ikari closely as the Commander had ordered her to. Commander Ikari had been adamant that she watch for any sort of abnormalities or unacceptable changes in either of her fellow pilots. Anything out of the ordinary she was to report to him, no matter how minor. As she looked at Ikari's image on the view screen, she could notice some subtle alterations in his appearance. Soryu was also changing slightly, so slightly that no one other then her could really notice.

"Dr. Akagi, are there any abnormalities being reported by the Magi with the nanites?"

Ritsuko was caught off guard by Rei's question. She hardly ever said much of anything if she wasn't being spoken to directly.

"None that the Magi are reporting Rei. Why do you ask?"

"I thought I saw something… odd on the monitor."

"I'm sure it's nothing Rei, the Magi are monitoring the nanites and will report any malfunctions. There really isn't anything to worry about."

Lt. Ibuki chose that time to speak up. "Doctor, the nanites have finished their cycle and are proceeding to shut down and dissolve."

"Very good Maya. Medical teams prepare to move the Pilots to the infirmary."

As the LCL drained from the test plugs, the medical teams moved to the exit hatches. When the hatches opened nothing appeared out of the ordinary at first glance. Shinji and Asuka were moved to the stretchers waiting for them and taken from the test facility to medical for examination. 

It would not be until their plugsuits were removed that the truth would be known.

--

Yui listened in stunned awe and horror at the tale of the initial accident. How could they have been so careless as to do something like that?

"We found out later that the test had been sabotaged. You're mother and I didn't really care though about how when we found out. We woke up in the infirmary rather refreshed and feeling better then we had for a while physically."

"And they never caught who did it?"

"There was a report of a tech that had been killed the same day, but the investigation into his death concluded that it had been a drug deal gone badly. We never really found out who was behind the accident, but I have my suspicions though."

--

The Technician stood in the alleyway located in downtown Tokyo-03 near the seedier districts. He had been told to be there by 2200 and it was now 2215. His employer was late, again. 

"Did you complete your task," a deep digitized voice asked from the shadows, startling the tech.

"Yeah, I did as you asked. Now I want my payment."

An attaché case slid across the ground to stop at the techs feet.

"Thank you."

Before the tech could leave the voice spoke once more. "One more thing. My employers have decided you are a loose thread. And loose threads, should be tied up."

A Glock 9mm with a silencer appeared from the shadows, held in a black gloved hand. Before the tech could run three shots were fired into his head and chest. The only sound heard outside the alleyway was the dull thud of the technician's body hitting the ground. The unknown man in the shadows left as unnoticed as he had arrived.

--

"So there were never any suspects?"

"Just the dead technician, but like I said I have my suspicions on who ordered it. Honestly none of that mattered to me at the time. When I awoke things were so different I had much more to worry about." 

Shinji took another picture out of the box and looked at it. It was a picture of him just after the accident. As he went to take a sip of his tea he noticed he had emptied the cup.

"I'm going to make another pot of tea, you want any?"

"No, I think I'll be fine dad."

As Shinji went off to prepare another pot of tea, Yui knew that she was anything but fine. This tale scared her to her very core, not because of what it might have meant about her father. That someone would plan out this sort of freakish accident made her wonder what kind of people had once headed Nerv, and what kind of monster her grandfather might really have been.

To be Continued…

Omake

The Technician stood in the alleyway located in downtown Tokyo-03 near the seedier districts. He had been told to be there by 2200 and it was now 2215. His employer was late, again. 

"Did you complete your task," a deep digitized voice asked from the shadows, startling the tech.

"Yeah, I did as you asked. Now I want my payment."

An attaché case slid across the ground to stop at the techs feet.

"Thank you."

Before the tech could leave the voice spoke once more. "One more thing. My employers have decided you are a loose thread. And loose threads, should be tied up."

A Glock 9mm with a silencer appeared from the shadows. Before the tech could run three shots were fired into his head and chest. The only sound heard outside the alleyway was the dull thud of the technician's body hitting the ground. The unknown man in the shadows stepped into the light revealing his identity. The killer took a cell phone into his flipper and dialed a number.

"Wark Wark." _It's done._

"Excellent Pen-Pen. You'll find a shipment of beluga caviar added to your usual payment."

"Wark WAaaaaark!" _Sure thing Lord Deathscythe_

In the dark secluded office of the Dark Lord of the Fics, Lord Deathscythe set his phone back on the table and contemplated this action. His associates Angel17 and Random1377 stepped into the office.

"You sure about this LD?" Angel17 asked.

"Yeah, I mean this is totally fucked up man, even for you." This from Random1377.

"I'm certain, everything is going according to the scenario." Said LD, looking at his fellow Darkscribes over his hands as he sat in the Gendo Position ™. 

The resemblance to Gendo Ikari at that time scared Random1377, Angel17 just shrugged it off.

"You done acting like some megalomaniac?" Angel asked.

"…Yes."

Authors Notes: Well, this completes Chapter 1 of my version of Claus's original idea. You may be asking why I decided to do something like this. Well, I always felt that there was a lot of work that could be done with this fic that Claus was missing, so I spoke to him one day about it. He had already decided to abandon his version so he gave me the go ahead to do mine. Originally I thought of going straight comedy, but my strong suit is doing drama. So I did it this way. There is more to come I assure you.

Special thanks to my pre-readers: Random1377, Angel17, TommyRude, Ken Sohryu, Shinagami, ShinRyuKen, and Weltall Elite, Myssa Elaine Rei and all the others were big helps in this first part. This time around Rakna tossed in some helpful advice as well.

C&C is always welcome at webmaster@darkscribes.org or ld25@msn.com

Later.


	2. Adjustment Pass the Blush Please

A New Life "LD Edition"

Chapter 2: Adjustment / Pass the Blush Please

By: Lord Deathscythe

Disclaimer: See chapter 1

As her father reentered the room, something disturbing occurred to Yui. If the story Dad had told her was true, and the photos appeared to be real enough, then that meant…

No, that was just too weird to even consider. There was no way it could be right… could it? Granted, the goings on at NERV would have seemed unusual to the people who hadn't been there, but this was too unreal.

Shinji placed a fresh cup of tea in front of his daughter, seeing the bewildered look on her face as she tried to come to terms with what he'd told her so far. He didn't blame her, not at all.

Shinji gave Yui a lopsided grin as he sat down in front of her.

"Yui, just so you know, that was the most normal part of this story. Wait until we get further into it: then you're really going to start questioning my sanity," Shinji said lightly. He chuckled as he pulled some more of the photos from the box. Most of the pictures were of the girl Shinji claimed was him, and some of the boy that he was telling her was Mom. It was frightening, but compelling all the same.

"It's… a little beyond unbelievable Dad. It's just not something that's really possible."

"There were a lot of things at Nerv that were like that. The Evas themselves were wholly unbelievable, and so was the idea of fighting giant monsters. Everything there read like a bad movie from the twentieth century. But the change that happened to your mother and I was much more difficult for us to deal with. Imagine that the body you've grown up with, changing beyond anything they teach you about puberty. Waking up the day after was one of the worst mornings of my life."

--

Misato stood outside the children's rooms awaiting Ritsuko's report on the experiment. The doctors hadn't let her see either Shinji or Asuka since they had been brought in, claiming that it wouldn't do any good. They had been even more adamant once Asuka and Shinji had been placed in their rooms that the head of Research be given first priority. 

This sucked.

Not only did it suck, but it raised Misato's suspicions. She was so preoccupied, that Kaji had no problems sneaking up on her.

"So, gorgeous, what's up?" Kaji asked, using the tone of voice he reserved for Misato.

"Cut that out, I've got problems here! They won't let me see how Shinji and Asuka are doing, and I have to wait for Ritsuko to show up before the doctors will even consider the idea."

"Perhaps they simply want to give Ritsuko their final analysis before they allow any factors to corrupt the experiment's results?"

Misato burned a bit at that comment, "Those two aren't just experimental subjects."

Kaji leaned against the wall, "True, but it is still in their best interests to let Ritsuko handle things for now. After all, the experiment was pretty risky."

"I know that, but it doesn't make me feel better about it though."

Misato and Kaji stood there in the hallway, waiting. That was the hardest part; waiting for Ritsuko to arrive.

The doctor walked up to them quickly, having received the initial reports from the attending physician. She didn't bother to speak with Misato or Kaji, entering Asuka's room and slamming the door behind her. 

Misato didn't even have the chance to look inside.

When Ritsuko exited Asuka's room, she shut the door with a stunned look on her face. Before Misato could even ask her what was wrong, the doctor quickly entered Shinji's room and slammed the door shut. Misato and Kaji just stood in the hall, staring at one other and wondering what was going on.

Ritsuko Akagi left Shinji's room with the same shocked expression, closing the door quickly behind her.

Misato and Kaji watched Ritsuko skim the file she had in hand, not saying anything.

However, Misato had run out of patience long before. "What the Hell is wrong with them?" Misato demanded. While she didn't know if anything was really wrong with her two charges, the way the doctors and Ritsuko were acting suggested problems existed. If something had happened, then someone was in for a lot of pain.

"I think we should talk before you see them," Ritsuko said, her voice dull with shock. This gave both Misato and Kaji pause, to wonder what had upset the doctor so much.

Whatever had happened to Shinji and Asuka, it couldn't be a good thing. 

"I want to see them NOW, Ritsuko."

"Misato, trust me. It's best if we talk first before you see them, before they wake up. This is going to be very difficult for them to accept."

--

Dr. Akagi led Misato and Kaji to the hospital's cafeteria, where she laid out the situation for them. Glossing over the more technical aspects of the issue, Ritsuko got straight to the point.

Misato didn't take the news very well.

"THEY WHAT?!"

Ritsuko stayed as calm as she could under the circumstances. It was difficult however for her to maintain this attitude, as what had happened was beyond anything in her experience. Even working with the Evangelions had not prepared her for this situation. If anything, it read like bad science-fiction. Kaji sat next to Misato, his mouth hanging slightly open in surprise. and his eyes a bit wider then usual. He pulled himself together while Misato began figuring out ways to hide Ritsuko's body when she was finished with the Doctor.

"We're still going through the data, but what it looks like is that, somehow Shinji and Asuka's DNA was altered in one chromosome. This chromosome was the one that determines gender. The nano-probes increased hormone levels in their bodies in order to complete the alteration. Also, their primary and secondary sexual characteristics have been changed. I think that the nano-probes digested the excess organs, and used that to recreate what was missing originally. While this is just a theory right now, is the most likely explanation." Ritsuko told them, all the while not deviating from her detached manner. However, Kaji noticed that the Doctor was nervously tapping her spoon against her coffee cup.

Misato was not so easily appeased. 

"Then why didn't the MAGI alert you in the first place? If this was a malfunction, then why didn't that failsafe of yours kick in?!"

"We're still trying to figure that out. Right now, what we know is this: Shinji and Asuka's hormone levels are still 200% above normal, and are more then likely to complete this transformation. Aside from the physical and genetic alterations, the Children are perfectly healthy. However, I'm concerned that the increased hormone levels will affect both their psyches and piloting abilities. Their hormonal levels will hopefully return to normal within two weeks, and the changes completed by the end of the month."

Misato slumped in her chair, tiredly rubbing her temples. Killing Ritsuko wouldn't help the Children now, and she was the only one who could return them to normal.

Kaji decided to voice something that was troubling him. 

"Has there been any investigation begun into the equipment? Just to be sure?" he asked.

"I've already ordered the equipment checked. That should be done by the time I get back to the lab," Ritsuko answered.

Misato had calmed down enough by this point enough to think clearly. Shinji and Asuka had been… switched from the sex they were to the opposite of that. This was not going to be easy on them, especially Shinji.

"How long until you can try to change them back?" Misato asked.

"I'll be ordering the lab to begin growing two more batches of the nano-probes. Depending on certain factors, it could be anywhere between three months to a year before they're ready. Right now, all we can do is deal with this situation and help them through the change. Try to keep things as normal for them as you can, Misato, and do your best to help them adjust. I had them put into separate rooms as per standard procedure, so they wouldn't contaminate each other's results. Considering the situation, this is for the best. I think one of you should be in each room, when they wake up."

This wasn't going to be easy at all.

--

Misato and Kaji split up, with the Major entering into Shinji's room and Kaji taking Asuka's. Kaji sat down beside Asuka's bed and looked at the Second Child, wondering when the changes would be noticeable. He could already see some of the changes in Asuka's face and was hoping that she… he wouldn't have too difficult a time adjusting to them. But that was going to be the easy part; the hard part was accepting the concept.

Kaji was drawn from his contemplations as Asuka stirred. Time was up.

Asuka slowly woke, feeling relaxed and better than she had in a long time. She even felt a lighter, as if a great weight had been taken off her chest. Wait… her chest did feel lighter. The familiar weight of her breasts weren't pressing down on her body like it should have. Tentatively, Asuka opened her eyes and looked down at herself.

Kaji had to put his hands over his ears to muffle the scream.

Asuka couldn't believe her eyes. What had those… those THINGS done to her?! If that wasn't enough, Asuka felt the presence of something absently rubbing against her leg as she sat up. With a hint of fear, Asuka picked up the blanket and peeked under her hospital gown.

Kaji would swear that some of the glass in the room had cracked, and was almost certain that his ears were going to start bleeding soon. The situation was fast getting out of hand as Asuka looked at her… himself in horror and tried to put it all together. She had graduated college at the young age of 13, was the best Evangelion pilot, and had seen monsters the size of buildings and had never even blinked.

All that was forgotten as Asuka Langley Sohryu realized that she was no longer the prettiest girl in school, but was now a rather unremarkable boy.

"Wha… What happened? WHAT HAPPENED?!"

Asuka began using every curse she knew in every language she had at her command, some of them sounding as if she had combined languages for the proper feeling. 

Kaji decided this was the time to step in. as much as he dared, in fear of his life.

"Asuka, calm down," Kaji spoke in as light a voice as he could, considering the situation.

Asuka didn't appear to like that idea. "Calm down?! How am I supposed to calm down when I've just been… been… WHATEVER THE FUCK THIS IS?!"

Kaji was a patient man, which was good as Asuka's hormones were ruling HIM now. Fourteen years worth of testosterone pumped through his body all at once, and there was no stopping it. Kaji was happy he was in here with Asuka instead of Misato, as Katsuragi was not renowned for her patience or tact. She was best suited for handling Shinji at the moment. 

Kaji knew he'd got the better end of this deal, because right now Shinji had the same amount of estrogen flowing through his… her veins at this moment. 

The agent also knew that remembering that the Children were no longer the gender they were before was going to be a nightmare. The pronouns were going to take some getting used to.

--

Next door, matters weren't progressing any better. Shinji was awakened by Asuka's first scream, and had Kaji not been momentarily deafened by Asuka's second one, he would have heard the horrific cry of the Third Child. Misato herself wasn't as lucky, and made a mental note to have her hearing checked later.

Shinji had awoken, feeling just as relaxed as Asuka had been, and as physically well as ever. But he'd noticed something odd; his chest felt as if someone was pressing down on it, and the gown seemed like it was hanging on him. Almost as if it were being held up somehow... There was also an odd tingling sensation in his chest, not quiet an itch but enough to make him try to scratch it away.

When his hand moved down, he felt some sort of… lump on his chest. Two lumps actually. 

Two lumps that tingled when he squeezed them.

Misato watched the whole time, and had the situation been less serious, she would have teased the Third Child about it. As it was, she was hoping things wouldn't be too bad when Shinji actually opened his eyes.

God seemed to be taking a coffee break at that moment, as her prayers were not answered.

Shinji came awake with the tingling still in his chest, and as his eyes opened he saw Misato staring at him with a look of concern mixed with fear, "Misato? Is everything okay?"

As much as Misato wanted to say 'yes', she couldn't. It had only been a few hours ago that Shinji was male... now he, no she, was lying in bed asking if something was wrong. Some seconds after Shinji asked Misato the question, he looked down and discovered what those lumps were. Just as Asuka did, he lifted the covers and noticed that something else was missing. 

"Mi...Mi... Misato?!?" He started to shiver as he looked over to her hoping that this was a nightmare and that he'd wake up from it, but it seems that Misato had the same face of worry on her and she shook her head. He was no longer himself... he was a woman.

Misato could only stare back at Shinji as she discovered the changes, the latter suddenly going into hysterics as Shinji shook her head and tried to wake from the very real nightmare, "Shinji." Katsuragi watched as Shinji looked to her, tears welling up in her blue eyes, and the Major wrapped her arms around the young 14 year old girl to try and console her.

It didn't help Shinji very much, as the feel of Misato holding HER felt so alien. The Third Child's body didn't feel like his… her body anymore.

Shinji screamed.

--

"It was a strange thing, to wake up in a body that wasn't your own anymore. It was made all the worse by the fact that we had in fact been normal only a few hours before. Things didn't get any better for a long time after that. Looking back, it seemed to be when everything began to go to Hell. It wasn't just the change itself that hurt."

Yui looked on her father as he continued his story, wondering how he could have handled that. She knew that the war had almost destroyed both him and mom. This, however, was beyond anything she'd ever conceived. Her father and mother had suffered through something that probably contributed a great deal of stress to what they already had to deal with.

"For the next two weeks, we were poked and prodded while the doctors tried to make heads or tails of what had happened. But, except for the development we underwent at because of the recent change, we were both completely physically healthy children. After it was over, I read a report Ritsuko had written to the commander about the accident."

--

"From what we can tell the change has been a complete one, from DNA to hormones to skeletal structure. Shinji and Asuka are perfectly healthy physically, but I wouldn't hazard a guess to their mental states."

Gendo sat at his desk, taking in the information as best he could. Fuyutsuki stood stoically behind him. After all they had seen since Second Impact, the event itself was not enough to cause either of them to be shocked. This did not mean they were unconcerned.

"Doctor, how will this affect their piloting?" Gendo asked, needing to know if his fighting force had just been reduced to one capable pilot.

"We haven't run any synch or harmonic tests with them yet. I've been waiting until their hormone levels to smooth out so we can get a representative test. Once they have been cleared to return home, I'll begin scheduling activation tests with Unit's 01 and 02. Right now, I'm expecting at least a ten point drop due to mental stress, but that can't be helped. Aside from that, there are issues with their motor coordination, even concerning things as simple as walking." Ritsuko replied. She didn't let on how she felt about the Commander's preoccupation with their piloting responsibilities: it wouldn't have done any good.

Fuyutsuki spoke up next, "Why would there be a problem, Doctor?"

"Due to the modifications to their skeletal and muscular structure, both Shinji and Asuka will have problems with balance, movement, and anything involving physical activity until they adapt to the shift in their centers of gravity."

"Any progress on the investigation, Doctor?" This came from Commander Ikari.

"Right now, what we've been able to determine is that the feed tubes from the nano-probe tanks were intentionally switched. When the nano-probes came in contact with an unexpected organism they attempted to adjust the organism to be more like what they expected. I'm working on developing a new batch to reverse the alterations as quickly as possible, but it'll take time." Ritsuko concluded.

Gendo sat there, his chin resting in his hands contemplating all the implications this had. After a moment he dismissed Dr. Akagi to her duties, leaving him alone with Fuyutsuki.

Kouzou had one question on his mind right then. "So, how do you think Yui is going to take the fact her son is now her daughter?"

"This was unforeseen, I do not think anyone even considered this a possibility when the Scrolls were first written, or when Keil and the rest of Seele created the initial scenario. Things could become very difficult, especially if the Third Child breaks. We must adjust our plans accordingly. Perhaps this will act as a benefit rather then a hardship."

"You still haven't answered my question Ikari. What will happen once Shinji gets back into Unit-01?"

Commander Ikari stood and walked over to the window, gazing out unto the Geo-Front, "Nothing, we have simply altered the body. We cannot as easily alter the soul in such a fashion."

Fuyutsuki joined Gendo at the window, "For all our sakes, I hope you're right." 

--

Yui sat there, taking in what her father had just told her. It was the craziest thing she had ever heard in her life, not counting the things she knew of the Evangelions and Third Impact itself. Her father and mother had switched roles, so to speak, due to some experiment her Aunt Ritsuko had been performing. This wasn't something you really heard of every day.

Unless you're from Tokyo-03. 

Shinji was sipping his tea thoughtfully, collecting his memories for the next part of the story. He had never truly intended to share this with his daughter, but now he felt as if he had to let it all out. To let her know part of what had happened during the war. To let her know how she had truly come into this world. 

To tell her that he remembered...

"What was it like?" Yui asked in a soft whisper. She didn't wan to disturb her father too much from this tale, but she found herself pulled in. She was morbidly curious about this, like when one sees a disaster and can do nothing but look in horrified fascination. She wanted, NEEDED to know every detail.

Everything.

To be Continued…

Authors Notes: This was a very difficult chapter to do. Especially with Shinji's reactions to the change. Ryan Splicer had a hell of a lot of good ideas and was a big help. Thanks man. Also, I had difficulty deciding just how much I needed to get into the chapter. There is a ton of stuff I want to do with this, and not much time to do it in without each chapter becoming something of a gargantuan effort in and of themselves. I will be going into more depth about the change, how they handle it, how their friends deal with it, and how it affects the entirety of their world and the Angel War. This is going to be difficult, but rewarding in the end.

Pre-Reading props go to: Ryan Splicer, Typo, Revd, and Myssa. Thanks guys, I don't know if I could continue this without you.

C&C is always welcome at webmaster@darkscribes.org

Later.


	3. A Body Not My Own

A New Life (LD Edition)

Chapter 3: A Body Not My Own

By: Lord Legato Deathscythe

"What was it like?"

A simple question. One of the first questions a person asks in their life after why. It is a simple, four word question asking someone to define an experience that you never had before. A question you ask when you don't have anything to compare something to in your own day-to-day monotony. 

Yui and Misato Ikari had asked that question of their parents many times when they were growing up. They'd ask when they didn't understand something Dad would tell them about when he was fighting during the Angel War, when Mom would tell them about piloting an Evangelion. As they grew older, they asked the question wanting to know how it had felt to fall in love, to graduate school and college, to get married.

Things they had expected to do themselves one day.

Now, for the first time in a long time, Yui asked her father the same question. Not out of curiosity or an interest in the future, but instead to try to make some sense out of this story she had heard. To try to put some of the pieces together.

To understand the implication of the first photograph she had been shown.

Shinji sat there, choosing his next words very carefully. He looked in to the half-empty teacup as if the tealeaves would hold his answer. 

The tealeaves however refused to speak to him.

"It's impossible to describe something like that. Even to this day I can't come up with a good way of putting those first few days into words. It was beyond anything I could say. All I can tell you is that I barely held onto what was already a thin rope,' Shinji said, his voice starting to shake some as a lone tear fell from his eyes.

--

Shinji sat on her hospital bed, the same way she had for the past three days. After her awakening, she just stopped talking and did nothing but stare at the wall. The doctors were worried about her health, as the young girl hadn't eaten anything in that time. Nor had she even gotten out of bed, only moved to sit up or lay down depending on if she were sleeping or not.

It was on the fourth day Shinji moved.

She slowly got out of her bed, shivering as her bare feet touched the cold tile of the hospital floor. Slowly Shinji shifted her weight on to her legs, and almost fell to the ground. She quickly grabbed hold of the rail of the bed to steady herself, and then started to walk to the bathroom. 

It was slow going. Every step Shinji took was uncertain, and the poor girl felt as if she would fall over at any minute. Shinji's entire body continued to feel alien to her, even though she'd had four days to adapt to being female. Shinji did eventually make it to the bathroom door, grabbing hold of the knob to steady herself. Shinji opened the door and entered, turning the light on almost on instinct.

Shinji went to the sink and ran some cool water over her hands. She splashed some of the water on her face to help cement herself in reality. The cool water bit into her skin.

Shinji hadn't taken a good look at herself, and the first thing Shinji took into account was that her hands looked more delicate. The fingers had grown longer and slimmer than before. 

Shinji gasped in surprise as she looked up into the mirror.

The face there was still the face of Shinji Ikari, but it had changed as well. While the changes were very subtle, and almost unnoticeable, it was their subtlety that made them all the more magnified. There was a slight heightening of the cheekbones and a softening of his jaw line. Her skin had taken on a creamier color and it was softer and smoother to the touch. Other than that, it was almost like nothing had happened to Shinji Ikari.

Looking further south however proved differently.

Four days had passed, and the changes in Shinji's body had continued unabated. Shinji could tell her figure had filled out some more from when she had awoken. While it wasn't near Asuka's yet, the modest curves of her body proved that this hadn't been some horrible nightmare. 

Shinji was a girl.

_"__Great__, I bet Kensuke is going to try to sell pictures of me now as soon as he finds out what happened."_

For a moment Shinji couldn't understand why the thought of Kensuke's picture business came to mind. Maybe it was just something to take her mind off the fact that she was a she? A way of protecting herself from the truth of the matter.

Of course if the growth of her body didn't stop soon, there would probably be several boys wanting to get their hands on those pictures.

Whether it was the stress, mental fatigue, or just the idea that she'd end up being the young equivalent of Misato, Shinji didn't know. 

But that didn't stop her from laughing for the first time in a long time.

--

One room over, things were not as calm. Asuka had already gotten used to the change in his center of balance, and could walk just fine. This also meant he could get up and chase or attack the hospital staff that tried to poke and prod him. They kept insisting this was for Asuka's own good, but Asuka didn't believe one word of it. He knew what they wanted.

Look at the freak. Look at what's happened the Second Child, once the most beautiful and talented girl in school. Now she's nothing but an unremarkable, incompetent, scrawny little boy. Asuka isn't a she anymore; she's a he.

_"DAMNIT!__ HOW could they DO this to me? I bet Shinji came out just fine, same boring little boy as always. Of course the great Third Child's luck would never run out!"_

Asuka prowled around the room like a caged animal. The constant movement had helped him get used to this new form, and he could see the changes becoming more pronounced with each passing day. The hardening of the edges around his face was the most telling of the change. Whenever Asuka looked into the mirror, he could see signs of what had once been the face of a beautiful young woman.

Truly, now Asuka Langley Sohryu wasn't a little girl anymore.

--

Two weeks passed by almost too quickly, and from what Ritsuko could tell the external changes to Shinji and Asuka had been completed. It was odd how the change had taken half the time the doctor had expected, but things happen as they happen. The Children's physical check-ups showed no ailments, or anything out of the ordinary…

At least anything not more out of the ordinary than the situation already was.

Ritsuko had already reported to Commanders Ikari and Fuyutsuki concerning the eminent release of the Children. They had been less than responsive, as usual. As long as she had scheduled synchronization tests for the Children than they were unconcerned. Typical.

Misato and Kaji however were a different matter.

They had been informed of the Children's release as well, and now all three were in Ritsuko's office trying to figure out their next course of action. 

Getting Shinji and Asuka home, and reintroducing them to each other.

This was going to be fun… like taking Unit-01 to the dentist, or trying to tell Commander Ikari he owed late fees to an adult movie store.

Misato sat across from Ritsuko while Kaji stood leaning his back against the wall. 

Misato was pretty clear on what she thought should happen.

"They're coming home of course!" she shouted.

"I'm not so sure that's a good idea. Shinji and Asuka are still in very unstable psychological conditions. I still think we should keep them within the Geofront until we render the changes back. It's best for their security and their health," said Ritsuko.

"Yeah, leave them in the hospital for 6 months when there isn't anything really wrong with them now. That will help, having them poked at like lab rats. You do that enough to them when they're in the Evas. They need time away from all that if they're going to be able to function at all. Let alone when we need them to pilot in a serious combat situation."

Kaji listened to the two women go back and fourth about the situation. He knew Misato's blatant concern for the Second and Third's combat readiness was a simple ploy she was using against Ritsuko. It was a classic battle, one where the combatants both had the same goal in mind. The best interests of Shinji and Asuka were central to both their positions. They just disagreed as to what those best interests were.

Kaji decided it was time for him to step in.

"Now ladies, we should think of this rationally. Now, the children are going to be stuck like this for some time. And we don't even know if we can change them back at all, let alone when we'll be able to. So I think it's best if we try to keep things as normal as possible. If only just sending them back home so they can be a bit more comfortable. Don't you think Ritsuko?"

Ritsuko didn't like it when he was right. Section 1 had been having troubles growing the new batch of nano-probes from the start. For some reason the nano-probes kept coming up malformed or too big. Either way they weren't going to be doing anything if these problems kept up. Keeping the Second and Third in the Geofront for an extended period of time without a guarantee of success would make things much more difficult in the long run.

They had planned this, Ritsuko was certain of it.

"All right, we'll send them home. But I don't want them making any unnecessary trips outside the apartment. This includes school, especially. We don't want them having to answer any questions from anyone about this." Ritsuko said.

"And what about their classmates, what are they going to think after a prolonged absence? I know their friends are at least going to try to find out what's happened," Misato replied.

Ritsuko countered, "Look, if you have to tell anyone keep it to an absolute minimum. See if you can get Rei to help you out with that. Just keep things controlled and stable as much as possible. Oh, and I'm going to have some extra funds deposited to your account Misato."

This confused Misato. Why was Ritsuko giving her more money?

Knowing the question before it was asked, Ritsuko answered, "You're going to have to do some clothes shopping. I doubt that either of those two have anything they can wear. I suppose Asuka could use some of Shinji's school uniforms but you know she… he won't want Shinji anywhere near… HIS wardrobe."

This was going to be interesting, and not in the "ooh and ahh" way. 

Interesting in the "this is totally fucked up" way.

--

Kaji and Misato had once again decided to split up and take the two home; separately. They figured that with everything that had happened it was best to hold off their meeting as long as possible. They both felt it was best to prepare them for what they would be seeing when the other entered the same room. 

Kaji wondered to himself, just exactly how extreme this change was. If it was simply the body or if other…traits had changed accordingly. He grinned as he thought of the possibilities. One of which came to mind, causing the agent to shudder. He certainly hoped this change was extremely thorough. 

Otherwise he'd be in a very ugly situation.

He walked to Asuka's room, and steeled himself towards the possibility. He prayed to the Almighty that this wouldn't happen. He didn't enjoy fending off Asuka as a girl. Fending Asuka off now as a boy would just be too freaky for him. 

If all was going according to plan, Misato should be half way to the apartment right now with Shinji. The Purple haired goddess of Kaji's life would have enough to deal with when it came time for certain details of Shinji's new life.

One of those "details" that all men feared most above all others: probably the only thing that could scare Gendo Ikari and all of Seele.

--

The blue Alpine Renault pulled into the parking lot of Misato's apartment building slowly, coming to a stop with its two travelers. Shinji and Misato didn't get out of the car immediately, they just sat there for a moment as the engine cooled. Shinji sat there with her hands in her lap staring at the fabric of the pants she was wearing. Fortunately Shinji didn't need to worry too much about clothing yet. The school uniform the Third Child had been wearing the day of the accident was good enough to get her home, but the underwear Misato had brought felt odd.

Or perhaps it was the absence of a certain part down below Shinji was noticing.

Misato looked at the forlorn expression on Shinji's face, and placed her hand on top of the young girls. She gave it a soft squeeze as Shinji looked up at her. Misato couldn't read the mind of the young boy turned girl, but in this case she didn't need to. It was all written on Shinji's face. The uncertainty of the moment, the confusion, and fear just beneath the surface could all been seen in the eyes of Shinji Ikari.

"Come on, let's get you in the apartment. You'll feel better after a bath and a change of clothes. I think I have some sweatpants that are just your size. After that we can talk about what we're going to do okay?" Misato said.

Shinji looked at her, nodding weakly as they got out of the car. When they had entered the elevator to go up to their floor Shinji asked, "Where's Asuka?"

It had been something that for some reason had been tugging at the back of her mind. The Second Child hadn't so much as come to laugh at the Third Child's plight. This could have been something that Ritsuko had a part in. Since Asuka had also been a part of the experiment it was safe to say she had also been under observation.

Of course, knowing Shinji's luck Asuka was in fact still a she. 

"Uh, Shinji, we're going to need to talk about that. Asuka, well you'll get the idea when you see him."

_HIM?!___

"Asuka got switched too… didn't she?" Shinji asked. She didn't need an answer. It seemed pretty obvious by Misato's slip of the tongue, if it had been such.

"…Yes." Misato answered. Maybe it would do Shinji some good to know that she wasn't alone in this little bizarre nightmare. But then again, whose sick mind could come up with such a scenario? Even for a dream?

They got to the apartment and Misato let Shinji go get in the shower while she got together some clothing for the lass. Misato had found a pair of sweat pants, a loose fitting shirt that wouldn't show too much, and raided Asuka's underwear drawer for a pair of cotton panties and a plain white bra Asuka wasn't bound to miss. 

She thought twice about the bra. Shinji probably wouldn't be the same sizes as Asuka, but it was best to let her have some practice putting the supporting wears on. That could be a little fun.

For Misato that is.

Shinji lay back as the hot water eased some of the tension out of her muscles. Bad memories always followed Shinji to the bath, but this time none came. Shinji was living one right now. However Shinji did feel a bit better after finishing the bath.

She put on a soft robe Misato had given her and went to her room. Misato stood there holding the clothes she had managed to find, hoping they were the right size. The sweatpants from her closet though were going to be a bit baggy on Shinji. Not that Misato was fat or anything, but she was older and had grown more then Shinji had. So it was to be expected that her hips were slightly wider then the any girl of fourteen years old.

As expected though, it was all easy until Shinji called through her door.

"Uh, Misato, I don't know how to put this bra on," Shinji timidly called out.

Let the games begin…

--

Asuka sat quietly in the passenger seat of Kaji's car. It was similar to Misato's but in a black color. Asuka hadn't said much since Kaji had entered his hospital room, and had been uncharacteristically quiet throughout the entire trip. Kaji was concerned that Asuka maybe falling into a depressed state. And with Asuka, that was like a volcano sleeping until it one day explodes in an impressive and deadly display of lava and ash.

Something that would be the worst possible event for everyone involved, especially Asuka.

"So, how do you like being a boy so far?" Kaji asked with a hint of his usual merriment in his voice.

"It sucks. I'm all scrawny and boney. I don't look as good as I used to. I'm not even much to look AT!" Asuka replied. He was aggravated all the more by the fact that being a boy would make getting Kaji to understand her… HIS love for him was truly impossible.

Kaji didn't swing that way.

"Shinji probably came out the same wimpy little boy he went in as. At least the apartment will be able to support normal living beings. I'd hate to see that place if Misato was left on her own for more then three days."

Kaji decided to lighten the atmosphere of the car a little. Misato would understand. "You didn't live with her back in college. She couldn't be bothered to clean to save her life. Ritsuko always complained about the chaos Misato surrounded her self with. Ritsuko once told me that if left to her own devices Misato could destroy an entire city just by living in it and not cleaning up after herself."

Asuka chuckled a bit; not a out and out laugh but it was still something.

"Maybe I can at least get Shinji to cook up something good tonight. He maybe housebroken, but he's a damned good chef," Asuka said.

_"Might as well tell him now,"_ Kaji thought.

"Yes, SHE is a better cook then Misato ever was."

Asuka stared ahead. _"SHE?!"___

"Shinji also has to deal with a few problems now. But at least you both get to find out how the other half really lives."

"SHINJI'S A GIRL?!" Asuka screamed out in shock, than broke down into laughter for the first time in a long time.

Kaji let Asuka laugh at Shinji's misfortune. It was a way to get Asuka to accept his own situation.

"You laugh now, but just wait," Kaji said with a big grin.

"What do you mean?"

"You know all those jokes men make about a woman's time of the month? Well you're going to learn first hand WHY we make those jokes," Kaji said, his grin growing even bigger.

Asuka didn't understand… yet.

--

The two males arrived at Misato's apartment without incident and let themselves in. Kaji wanted to talk to Misato before leaving to discuss some things and coordinate anything Shinji and Asuka may need. What they walked into however was peculiar to say the least.

And since they couldn't actually SEE what was happening, could have been taken the wrong way.

"Ouch, Misato I'm telling you this is too tight!" came Shinji's voice.

"I don't get it, this should be much looser then this," this time Misato's voice. 

"Well it's not, it feels like your trying to crush me to death."

"Oh it's not that bad."

"Says you, and stop touching me there, he he, I'm ticklish."

Kaji and Asuka blushed, profusely.

They wouldn't be… doing THAT now would they?

Just then Misato and Shinji stepped out, with a white cotton bra in Misato's hands and Shinji wearing a loose shirt that left most everything to the imagination.

"I swear, it's not possible for you to have bigger breasts than Asuka. There is just no way," Misato, said confounded.

"I'm sorry, but I don't even know what goes into figuring out sizes for these… things," Shinji said, pointing to her breasts as Misato and she stepped into the living room where Kaji and Asuka were waiting. Kaji let out a nervous laugh as Misato glared at him. She didn't need to ask; she knew exactly what he had been thinking.

Shinji and Asuka however ignored the two. They just stared at each other trying to find a hold on the moment. Here they were, two people who had been so use to the way the other looked, moved, sounded, maybe even thought now changed on such a fundamental level.

Asuka's face had hardened with more masculine features. His eyes and cheekbone had lowered slightly and all the appearances of the young woman Asuka had been growing into had vanished.

Shinji also had changed, from the scrawny young man he had been into a developing thin young woman. Most noticeable were the facial features having smoothed out more, and the addition of the breasts of course. 

It was like seeing the other for the first time all over again.

Minus the windy flight deck and unscheduled peep show of course.

"Let's go to the kitchen, I need a beer," Misato said, breaking the quite accord the two children had.

--

"So we're stuck like this for the next six months?" Shinji asked quietly.

"More or less, it all depends on how fast Ritsuko can make more of those nano-probes. And even if she can get them ready faster, she still needs to figure out if they can even reverse this. It was a possibility that no one even looked into before. Now that they are they need to see if they can repeat it without hurting the two of you." Misato answered.

They had all sat at the kitchen table, a beer in Misato's hand, and tea for the other three. Shinji and Asuka were still quiet, save for Shinji's question.

"But the good thing is, for now you don't have to go to school. I'll be speaking with your principal tomorrow about the whole thing. For the most part I want you two to avoid going outside except when necessary. Pretty much just when an Angel attacks or to do some light grocery shopping."

"So we're stuck here under house arrest too?!" Asuka said.

"Not so much. I just figure it'll be easier for you two to deal with things if you don't have to worry about being seen in public. But if it makes you feel better I could always invite your friends to come over and keep you company." Misato replied, knowing Asuka's reaction.

"YOU THINK I WANT THEM SEEING ME LIKE THIS?!"

That was what Misato expected.

"It's going to come out anyways Asuka. They are going to start worrying when you two don't show up for school soon. Hikari called twice yesterday asking about you and Touji and Kensuke have been coming by the apartment for the past five days trying to find Shinji. You can't keep this from them for long." 

"She's right Asuka," Shinji's quiet voice said.

Asuka knew it too, but didn't like the idea of his best friend coming here to find the great Asuka Langley Sohryu little more then a perverted male. 

But Asuka didn't know if he could go too long without seeing his friend.

"There is some good news though. I'll be taking you two shopping this weekend!" came Misato's enthusiastic sound.

"Shopping?" Shinji responded with some trepidation. The urge to shop it seemed was NOT part of the female genetic makeup. This was proven when Asuka brightened up and went on about finding the right type of cloths and shoes to wear.

Shinji felt like hiding for a month right then.

--

It was late, very late. Shinji had been lying in her bed for hours just staring at the ceiling. 

Her bed, not his bed. Not anymore.

Shinji had gone to bed wearing the clothes Misato had given her earlier. They were very comfortable and in a way helped calm Shinji down. But it didn't do much to keep her mind calm. Even with the soothing music of Beethoven floating through the ear buds did little to push back the sickening reality that she may be forever stuck as a she. 

Granted, Shinji had more pressing things to worry about and have nightmares over, but this was just one more bad turn on a horrible ride.

Eventually, Shinji could probably come to accept it.

But for the time being it was impossible to fathom being a female for the rest of her life. It just wasn't something Shinji had ever considered. Now the Third Child had to face the now overwhelming possibility of being a female and all the things that involved. 

Shinji looked at her clock, and saw that it was already six o'clock in the morning. She decided to get an early start on the day and went to the kitchen to make some tea. 

Asuka was already at the table, a cup of tea in his hand as well.

Neither spoke as Shinji made her way to the stove to prepare her tea. Asuka turned his head to watch Shinji as she stood there. Shinji didn't notice Asuka looking at her, and tried hard not to look back at the red headed boy at the table. Asuka looked on, taking in every feature of the new Shinji Ikari before him. The Shinji Ikari that now had a female's body as he now had a male's body. Asuka knew Shinji was trying to avoid looking at him.

If only to pretend for a moment that they were both normal.

Shinji sat at the table across from Asuka. Asuka adjusted his line of sight from Shinji's head down to her chest. That had been a shock for him, to find out that Shinji had been gifted with a larger bust then he had had. But there was something else behind the young boys look.

Longing some would say. Longing for this whole nightmare to be over soon and a return to what passed for normality for the two. But there was something else.

"I don't get it," Asuka finally said.

"Get what?" Shinji asked, blushing when she noticed Asuka's line of sight.

"I don't get why boys are always staring at my chest. I'm a boy now, shouldn't I be noticing something?"

"I don't know. I honestly never thought much about it. I've only really looked at Misato's, and it's not like I had much of an option at times."

Asuka smiled lightly, "She doesn't exactly hide it does she?"

"No, now I have to figure out everything. It's not easy."

"I've got it just as bad as you. I can't stand this body, and that damned penis of mine does as it pleases. It can get very uncomfortable at times," Asuka said.

"I know. But I think you'll have a bit of an easier time getting used to that then I will."

"Oh and how do you figure that?"

"Remember the bra?"

They both had a small laugh at that.

"Yeah, I remember."

They fell into a comfortable silence. Neither had much too really say. 

They just fell into the moment and for a time were two normal (relatively speaking) children.

And that was just fine with them.

--

"It was the first really peaceful time we had ever had together. Ever since I had met her we had never really gotten along. She'd be constantly upset over everything I did and I'd just back down and close up. That first night home though, we had enough pressing down on us. It was a chance for the both of us to just gain a handle on the moment. And it was that night that I thought for a moment, maybe there had been something there before between us."

 Yui sat before her father, the shock being replaced by rapt fascination. Some where down the line she had left her amazed speculation go and had become so intently wrapped up in her father's story, she craved to know more. 

In a way, it was like hearing the story of how Shinji and Asuka had fallen in love all over again. Yui had always loved to hear about the courtship of her parents. But that now was known to be slightly false. The first time she had asked her father about it, she felt as if she were actually watching her parents as young adults fighting and falling in love.

This story was just as captivating to her.

"It must have been weird," Yui said.

"It was. We stayed home for the next couple of days, just trying to get used to living like that. It was… interesting."

--

Misato was passing by Asuka's room on her way to the kitchen, when all of the sudden she heard the oddest exchange coming from behind Asuka's door.

"Listen, I don't like you, and you don't like me. But we're gonna have to find some way to get along if we're gonna make it through this alive," Said Asuka's voice

"Asuka, are you talking to your penis again?" Misato said in a teasing tone, and then ran as Asuka came barreling out of his room intent on doing physical harm to the Major.

--

"She said that?" Yui said through the laughter she had been consumed by.

"Yup, it was as if she were at war with it. It was a great source of amusement for Misato. You wouldn't believe the 'Little Asuka' jokes she came up with," Shinji answered, a grin on his face.

"I can't even imagine the look on Mom's face when she heard that."

"Well, it was something she learned to laugh at when she got older. That weekend however…" Shinji trailed off at that. 

"What happened that weekend?"

"Our friends were introduced to Ms. Shinji Ikari and Mr. Asuka Langley Sohryu. If you thought that last bit was funny, you're going to die laughing when you hear this."

--

They had just gotten back from the mall, and Shinji was tired. Misato had taken her all over the place having her try on outfit after outfit. It had gotten especially embarrassing when Misato insisted Shinji needed some items from Victoria's Secret. 

Shinji felt that some normal underwear was just fine, but Misato would not be stopped. 

Then had come the makeup. 

It had felt that they covered her face in goop.

Misato had sent Asuka out on his own to shop. As Misato had said, "Asuka knows how to shop for clothes. You need my help."

Help? More like Misato enjoying the chance to go on a shopping binge even if the clothes were all for Shinji. But she had to admit; some of those outfits did look pretty on her. And after a while she had actually started to enjoy herself. 

"Shinji, come with me," Misato said as she dragged Shinji and some of their packages back into the bathroom. Asuka just went in and put his new clothes away. As he did he saw the yellow sundress he had worn as a girl. In almost every picture where they had been having some fun Asuka had been wearing that dress. 

He ran his fingers along the fabric in silent reflection. 

Time to move on… but how?

Asuka was pulled from his thoughts by a knocking at the door. 

--

Kensuke, Touji, Hikari, and Rei had somehow met at the front of the apartment. Misato had called each the day before, but she hadn't told them anything about Shinji and Asuka. Rei already knew but said nothing. She had been asked numerous times over the past two weeks, but had not said. She was unaware if the Second and Third Children's condition was classified or not so she had erred on the side of caution.

"So what do you think Misato wanted to talk to us about?" Hikari asked.

"It has to be about Shinji and Asuka. Maybe they were injured in an experiment or something," Kensuke replied.

"But wouldn't she tell us if something had happened to them? They're our friends!"

"Not if it were classified."

"I don't think it's anything that serious. She sounded pretty happy on the phone when she called. If something had happened she would have been more serious," Touji said.

The four children arrived at their destination, M. Katsuragi staring at them from its humble nameplate. Touji knocked on the door as the four stood there, three of them pondering what awaited them on the other side. 

They had not expected two long arms to reach out and drag Hikari and Rei into the apartment. To the boys it was reminiscent of several tentacle hentai movies they had seen. Had they not been certain the arms that had grabbed the girls were human Touji and Kensuke would have expected to see shreds of cloth beginning to fly. 

It turned out that the arms had belonged to the very much human Misato Katsuragi.

As Misato dragged the girls off to the bathroom she shouted back at the stooges, "Come on in and make yourselves comfortable."

Touji and Kensuke just stared for a moment then stepped in, removing their shoes.

"What do you think that was all about?" Kensuke asked. Little did the duo know that they were being spied on: by the soon to be revealed male Asuka. 

Asuka didn't know exactly how to approach this situation. On the one part she could have just hid and then waited for them to leave. But… the possibility of causing severe mental trauma to two of the Three Stooges had its claws in his mind.

Hikari's shocked scream from the bathroom gave Asuka his cue. 

Touji and Kensuke were just about to run for the bathroom when a red headed man stepped out in front of them. The boy had blue eyes.

"Hello boys," said the new comer.

In a German accent: 

No way. No way in HELL!

There WAS a resemblance but could it be…?

Nah, probably just Asuka's brother visiting.

But she didn't have a brother, not one that she talked about anyways.

Touji decided to ask the question after his jaw was pulled back into is hinge, "Are you Asuka's brother?"

Asuka chuckled, that had been the most logical assumption Touji had ever really made in front of the Second Child. In fact, it could have been a great cover.

Had Asuka not blown it.

"Sorry, but I don't have a brother," Asuka replied.

Touji and Kensuke moved towards the Second Child. Morbid curiosity and shock had briefly overrode their learned response to getting anywhere within striking range of Asuka. Touji even went as far as to poke at Asuka's forehead to make sure that what they were seeing was in fact real. 

Asuka for his part just chuckled as the two befuddled boys continued their inspection. Were Asuka still female he would have already attacked them? It was taking an enormous amount of will not too right then. In the long term though, it would be something for him to laugh about after it was over.

If it ever WAS over.

Kensuke and Touji moved back and turned around, huddling together.

"So?" Touji asked.

"It could be a really good disguise. Some make up and a few prosthetics and Asuka could be made up to look like a guy. There's only one certain way to know," Kensuke answered.

Touji's blood ran cold. He could figure out pretty easily what Kensuke was thinking, and even as strong as he was the taller boy would never have dared try it. Kensuke was giving Touji a look that just screamed something dangerous that he had been volunteered for.

"NO WAY!"

"Come on Touji, if you do it then you have a higher chance for survival then I do. Also, if this is a guy then you don't have to hold back. If not, then I'll be sure to lay flowers at your grave every month."

There was no getting out of it for the athletically gifted lad. Kensuke was going to use every piece of logic and cajoling in his arsenal until Touji backed down, and Touji didn't have the brains to last long.

Touji would have to grope Asuka to confirm what they were really seeing.

Touji turned around and faced Asuka, but if you asked him he was facing death itself. He extended his arms and turned his head slightly, then started what could have been his final walk.

It was a long walk.

_"He's going to try to grab my breast! OH THIS WILL BE WORTH IT!" _Asuka thought.

Asuka wasn't going to attack Touji at all, and if you looked at his face you could see the red headed boy trying to restrain himself from breaking down in laughter.

Touji got within groping range of Asuka, and so far hadn't felt anything. All it would take was one step and then it would all be over.

"If I'm going to die, at least I'm going to die with something soft in my hands." Touji said. This was it.

Touji took a step forward, and his hands ended up FLAT against Asuka's chest. No bulging, nothing being held down. FLAT as a board.

Touji turned his head and looked at where his hands were. Upon confirming not only the fact he wasn't grabbing anything, but that he was in fact still breathing Touji jumped back as if he had been hit. His eyes had grown huge and some would say he had gone a shade paler then even Rei had accomplished.

It was true.

"ASUKA'S A GUY!" Touji screamed in shock and terror.

Kensuke joined Touji in shock and horror while Asuka began rolling on the ground laughing his ass off.

But if Asuka was a guy, that meant…

SHINJI HAD…

--

In the bathroom, Hikari had been considerably less touchy feely then the boys. She didn't need to. Shinji was sitting in the middle of the bathroom in her undergarments as Misato moved around her like a bee. Hikari took a moment and pinched herself to see if this hadn't been some sort of dream, or hallucination. 

When that was confirmed her brain decided a nap was in order, and Hikari fell in a dead faint.

Hikari slowly came to consciousness, her faint not having been too severe with a bad headache. She just blinked as Rei started down at her.

"Rei… did you see what I saw?" Hikari asked in a whisper.

"What did you see?"

"I'm saw a girl in front of me that looks like Shinji in bra and panties and Misato doing a makeover."

"Then you are seeing the same thing I am."

Hikari was shocked. Rei hadn't been surprised at all. But that didn't surprise Hikari as much considering that Rei would have already known.

"Hikari, give me some help here. Shinji's hair is not cooperating," Misato called to the teenaged girl.

After finally getting over her shock and off the floor Hikari slowly went into "Makeover Mode" as she liked to think of it and took some hair curlers.

Shinji could only hope Hikari would have a calming influence on Misato. She didn't want to end up a victim of her guardian's fashion sense.

Rei continued to stare.

--

It had been maybe an hour after the four young people had arrived at the apartment before Misato and Hikari introduced the fruits of their labor. 

Had they not know it was their best friend under there Touji and Kensuke may have started drooling right there on the spot. Asuka had already told them most of the happenings and why they hadn't been seen: The unclassified version at least.

Now Shinji stood before them, in a conservative white button up blouse and a blue skirt that went down to just above her knees. Her hair had been styled short, but framed the young woman's face nicely. The slight makeup also had brought out a little more of the exquisite beauty that Misato and Hikari had crafted like sculptors. 

And Shinji did have a very nice rack too.

They had all sat down and discussed things. How they would work out school and the like with finals fast approaching. And of course how they would try to keep as few people from finding out as possible.

It had degraded from serious discussion to another get together party of Misato's after that. The major had started drinking and getting a chuckle out of teasing the boys. 

Misato had a lot of fun trying to tease Asuka.

But at some point during the evening, Shinji had made her way out to the balcony. Even now she didn't like being around crowds of people.

Shinji stood out on the balcony looking at the city before her. While she was glad her friends had come to see her, Shinji didn't know how to act around them now. Before, they had talked about things that she didn't quite understand. Touji and Kensuke teasing her about staring at parts of Ayanami when she was still a he. How would they be able to talk that freely about such things again? How could Shinji hope to understand what they thought, now that he had become the group that was a topic of some conversations?

Shinji sighed, feeling even worse then when she had come out before. She didn't even notice the balcony door slide open then closed, or the steps behind her until Touji settled down against the bar to her left.

"So, how's it feel?" Touji asked.

"Weird. I can't really describe it; I just don't know the words. Two weeks ago everything was normal. I put on my pants and went to school. Now, now everything I feel feels amplified a bit. It feels like I'm being pulled in ten different directions and I don't know which way to go. I get the impulse to do one thing, but then I remember that I would never do that," Shinji said, desperation and sadness falling into her voice.

"Can't say I know what you mean, but then again who would. I don't think this has ever really happened to someone before, at least not like this."

Shinji looked out across the landscape, her thoughts coming a bit easier for the moment.

"Then, there's when I look in the mirror. It's me, but it's not me. It's not the face of Shinji Ikari anymore. It's like I'm just his sister or a completely different person. The only thing that makes it easier is that I can try to think that my mother looked something like this when she was my age. As if I've gained a part of her back because of this."

"Maybe, but do you really want to stay a girl just for that?" Touji asked, curious to if this would be something Shinji would remain for the rest of his… her life.

"No, I want to switch back. It's just…"

"Just what?"

"Just that I feel more comfortable now. It could just be me getting use to the changes my body went through, but I feel better about it now then when it happened."

"Sounds 'bout right. This will make things a bit more difficult though. Me and Kensuke can't tell dirty jokes around you or tease you about the girls anymore until you switch back."

"Even if they can't pull it off, and I'm stuck like this forever, we're still friends right?"

"Damn straight. You may wear a skirt now, but you're still Shinji. Besides, I kinda thought of you and Kensuke as brothers I never had. Now I guess I have a new sister."

Now, while Shinji would have never done anything remotely close to what she did next before the accident, her emotions did feel a bit more intense then before. To hear such words from Touji, her best and first true friend, she couldn't help herself.

And so, Shinji hugged Touji. This took Touji off a bit, quite a bit actually as Touji had never really been embraced like this from any girl other then his sister. Not like he was going to complain though. While he didn't show it much in public, he still had a rather soft heart for people he liked. Touji wrapped his arms around the girl who had been one of his best friends protectively almost. There was nothing romantic about the embrace, nothing signaling any sort of wish from the other. It was like two members of a family exchanging their feelings for the other. 

And Touji would be damned, if anyone hurt his family. He had gotten over what had happened to Mari a long time ago. While he knew Shinji would still be fighting the Angels to save all their lives, if anyone human tried to hurt her there would be Hell to pay.

Even if it was Asuka.

--

"After all was said and done, Touji was really my best friend. He never did think before he said anything, and even though at times it could get him trouble it also meant he was serious. He had meant what he said that night on the balcony, and after the Thirteenth Angel came it meant more to me then anything," Shinji said with a light smile. As he had gone on he had gained a sort of dream-like countenance Yui had never seen her father have before.

Yui sat there and watched her father, and hung there waiting for him to continue.

To Be Continued…

Authors Notes: ~Looks back over his writing~ O_O MY GOD IN HEAVEN! 20 PAGES! This must be the longest I've ever written for one chapter. But there was a ton of things I wanted to get into this to help move things along. Hopefully, after all is said and pre-read you'll all have a lot of fun reading it. I have to say, the entire process of thinking up and writing this thing is at times a nightmare. But when you get past things like pronouns and such, and focus in on the situations you want to present it starts coming out much more easily.

Thanks to my pre-readers: Ghola, Joedoebell, RagnarokZ, Myssa Elaine Rei, Angel 17, Random1377, and Rakna.

And remember, after the fic we will have a special OUTTAKE OMAKE CHAPTER!

But first… you didn't think I'd end the chapter without one did you?

OMAKE!

He hadn't intended for Touji to find out, but unfortunately Kensuke's luck just wasn't that good today. Usually he let the taller boy in on his schemes, and of course on any chance they'd get to sell pictures of the girls. But not this time. This time if Kensuke had let Touji know the pain would have been extreme.

Like the pain he was feeling right now due to the right hook Touji had just let loose on him.

"I can't believe you were selling pictures of Shinji! If I don't stop you now, soon you'll be fantasizing about her... I mean him!" Touji cried, indignation that Kensuke would sell pictures of the young… girl he considered a sister pulsing through his voice.

The silence and guilty look from Kensuke told Touji all he needed to know.

"Sweet Mother of God!!!" Touji screamed and then let loose another hard punch to poor poor Kensuke's gut.


	4. All the Small Things… Angelic Shadow

A New Life (LD Edition)  
Chapter 4: All the Small Things… / Angelic Shadow  
By: Lord Legato Deathscythe

Disclaimer: see part 1

"Things after that weekend returned to something resembling normal. As far as the school was concerned, NERV had decided that it would be better for us to be home schooled. Security matters were the perfect cover to keep unwanted eyes off us. We just studied, performed sync tests, went through combat training exercises, and somehow found time through all of that to be the children we were."

Shinji stopped for a moment and sipped his tea. It was a sordid affair, but it was somehow one of the happier times of his life. Not many good things had happened to Shinji or Asuka in their younger years. While the change itself was a living nightmare, there was some good to be found in those memories. Most of them were memories of a time when his best friend had been there through everything.

"Then about a month and a half later it happened… and dear God am I glad I changed back. Just thinking of that day is enough to remind me why I never made jokes about that."

Yui sat up and looked at her father, puzzled. "What happened?"

"The same thing that happened to you at that age. My new body decided that it was time for me to become a woman."

Yui got comfortable, because this was going to be good. It would probably explain why Dad was always so easy to talk to when it came to those kinds of woman troubles.

--

Touji had convinced Shinji to go with him to the mall. He knew that Shinji had been spending more time hold up in her room, and thought it would be good to get her out for a while for something not related to NERV. Besides, he wanted to buy something for his sister Mariko.

Shinji however wasn't looking so well.

"Touji, I have to sit for a bit. I haven't been feeling too well the past couple of days. I don't know what it could be," Shinji explained as she at one of the benches along the walkway.

"Have you seen one of the NERV docs about it?"

"No, it's probably just something I ate," Shinji replied. It was true that her stomach had felt extremely bad. Nausea had been her constant companion for the past two days.

Today was no exception.

Shinji put her hand over her mouth and moved to get up.

"Touji, I got to go to the bathroom. Now!" Shinji said with a gasp as she scrambled to her feet and fled to the nearest restroom hoping to make it to the toilet before her lunch came back to her.

There wasn't much Touji could do except feel stupid. He should have known better then to make Shinji come out in public at all. So he just sat there and waited for Shinji to return.

He waited for a long time.

--

Maya had just finished up in the toilet and was washing her hands and checking her makeup. Granted, she wasn't with anyone, but you never knew when you might run into a cute guy. Despite the rumor about her and Dr. Akagi, Maya Ibuki was as straight as an arrow.

A young girl running through the bathroom and into one of the stalls, only to throw up a few seconds later, catching the young lieutenant's attention. The sound of a person's last meal haunting them in the worst way followed.

"Excuse me, are you alright miss?" Maya asked as she walked towards the poor girl.

She was answered by the sound of some violent nausea. Maya didn't want to leave the young girl alone, so she went in and started pulling the girls hair from her face and holding it back.

That's when Maya realized who it was. She didn't say anything, instead choosing to just sit there next to the Third Child and ran her hand over Shinji's back. After Shinji finally emptied what was left of her stomach she curled up, holding her abdomen.

Shinji had never known pain like this on a physical level outside of an Evangelion before. It was so horrible all she wanted to do was curl up and try to forget it ever existed. It felt as if her intestines were twisting around inside and being pulled at like taffy. She thought throwing up would have made things a bit better, but she only felt worse and to add insult to injury… she was now starting to shake. Sweat started dripping from her brow as she tried to deal with the pain.

It was pure, unadulterated agony.

"Shinji, it's going to be all right. Just try to relax, okay?" Maya said as she looked through her purse. She had a good idea what was causing the poor girl's problems.

Shinji heard the voice, and didn't care who it was right then. All she cared about was making the pain stop. Every time she moved it got worse, so bad it felt like she was about to be torn apart.

Relaxing sounded like it might be the best option. Remaining motionless lessened the pain to the point that Shinji could open her eyes a bit and see Maya handing her some pills. Shinji took them and swallowed as Maya got her a cup of water. When handed it, Shinji took the water and drank what she could while Maya helped her off the cold tile floor.

When Shinji was sitting with her back against the stall Maya grabbed some tissue and started cleaning the teenager up.

"Shinji, what are you doing out here?" Maya asked. She didn't want to push Shinji too far, and honestly Maya wouldn't know how to reprimand a teen if her life depended on it.

Which, right now, it didn't.

"I came here with Touji. We were going to get something for his sister. I didn't think I was this sick, just some bad fish or something," Shinji answered, her voice strained and tired.

Maya just shook her head. Of course Shinji wouldn't know anything about this sort of thing.

"I'm going to take you home. Just wait here for a bit and I'll go get Touji. Then when we get to the apartment I'll get you situated and call Misato. You'll probably feel more comfortable talking about this with her. Trust me, you aren't sick." Maya said, and then got up to go find Touji.

"What do you mean?" Shinji asked. "I have to be sick if I'm feeling this bad."

Maya bent back down, a caring smile one her face as she placed a hand on Shinji's cheek. "You're not sick Shinji. This is just one of those things all women have to go through in their lives. I suppose you don't even have any pads. Well, I carry some in case of an emergency so I guess you're lucky."

Maya pulled out one of the pads from her purse and gave Shinji a quick and dirty explanation about what needed to be done.

Shinji turned a bright red color from the embarrassment. It wasn't just embarrassment though. Everything Maya told her about what was happening absolutely disgusted the Third Child. _Women actually have to do this?_

Shinji tried to forget about that for a while, and quietly dealt with the pain while Maya got up and went to find the young Mister Suzuhara.

--

Touji was worried.

Touji was very worried actually. Shinji had been in the restroom for at least twenty minutes, and Touji worried that she had been extremely ill. But he couldn't just waltz into the ladies room to check without being grabbed by a security guard.

The woman walking out of the restroom right then gave Touji an idea.

"Excuse me, miss?"

"Yes?" the woman asked.

"I was wondering if you could check for someone for me? She went in there a while ago and wasn't feeling too well. I'm starting to worry and I can't go get her. Could you check for me?" Touji asked.

Maya looked at the boy in front of her. Obviously Touji didn't recognize her, but that was understandable. They had only met once, and that was at one of Misato's parties.

Touji had been too busy arguing with Asuka to notice her at the time.

"Are you Touji?" Maya asked.

_I guess Shinji asked her to come find me, _Touji thought.

"Yeah, that's me."

"I'm Maya, I work with Shinji at NERV. Shinji isn't doing so well so I'm going to drive you both back to Misato's apartment," Maya said.

"So you know about the…?" Touji asked, wanting to make sure.

"I'm actually working with Dr. Akagi on the problem," Maya responded. They both left off what they were referring to – Touji because he didn't even like to think about it himself, and Maya because it was still technically classified.

"So, I'll go get Shinji and help her out. Then we'll get her back to the apartment and settled. That's pretty much my plan," Maya told the relieved teenager.

"Sounds good. I hope Shinji isn't too sick," Touji said, just as clueless as Shinji was.

"Touji, Shinji's not sick."

"Huh?"

"Shinji is suffering from… 'woman problems,' if you know what I mean," Maya said and left it at that.

The confused look on Touji's face told her that the boy had no idea what she was talking about. The young NERV tech couldn't help but chuckle at him.

"I suppose now's as good a time as any to figure it out. You are going to have to deal with women for the rest of your life, so you might as well learn how to deal with everything that comes with it."

_Boys_.

--

Maya and Touji helped Shinji up to the apartment. The poor girl, however, was feeling the worst she had ever felt in her life. Even including when _her _life used to be _his _life. Shinji just could shake the pain off. But there was more then a tug-o-war going on within her body's organs. Shinji was scared, confused, everything that a young girl going through her first period could be. The fact that Shinji used to be male however added a disturbing dimension to this.

As they walked into the apartment Asuka, who happened to be watching TV with Hikari at the time, looked up and saw the two bring in the bent over Third Child.

"What's wrong with you?" Asuka asked.

Suddenly Shinji burst out in the most emotional and angry display anyone could remember seeing from the usually timid pilot, "WHY DIDN'T YOU WARN ME ABOUT THIS?!" and ran off to the bathroom.

--

"It was the absolute worst thing I had ever felt in my entire life. The pain, uncertainty, and all of it wrapped in my male mind's disgust with the entire thing. I'm just glad it was Maya that found me and not some stranger. That would have been even worse. You are very lucky not to have had to worry about that, what with your mother and I pretty much knowing what we were doing."

Yui was suppressing some small amount of laughter. It might not have been funny at the time, but it sure amused her to hear how her father had been so clueless about the whole thing. And it gave her father a special perspective about what she had gone through at twelve. This entire story had also given Yui a new perspective on who her father had been. On who he had grown to become.

"Sounds like you had it pretty bad, Dad."

"I did. One of the things I was always grateful for when you were growing up was that your periods seemed to take more after your mother's than after mine. I was all twisted up inside and couldn't even move when that time of the month came. At least you and your mother could still do something. I was always laid up for at least three days."

Shinji drank a bit more tea and checked his watch, time for him to take his lithium.

"I'll be right back kiddo. Time to take my happy pills," Shinji said and stood up, going to take his medication.

While her father was up Yui took a chance to look at more of the pictures, each one an excursion into a hidden part of her parents past. Her mom hadn't made too bad looking of a guy, really. Even switched around as they were, Yui could recognize her parents out of their small group of friends.

It wasn't too hard with her mother: the red hair was a dead giveaway. And even then, the air of defiance and confidence she had always associated with Asuka Ikari was there. Her mother had been a strong woman, and had always loved her children. If anyone tried to get between Asuka and her daughters, they came away with the scars to prove you don't separate a mother and child. Yui wished her mother could have been there to see her baby when she was born.

Shinji walked back into the room, a plate of vegetables to snack on in his hands. She took a carrot stick as he sat done and bit into it as Yui took a piece of celery.

"Well, after that it was for the most part just a matter of sitting and waiting for it to be over. I just lay in bed with a warm pad over my belly and waited it out, getting up for food and going to the bathroom for the most part. Other then that not much happened, and it got slightly better each time I had to deal with it. But after a few days I was back in order for all intents and purposes, but then again you already know how that is," Shinji said.

Yui could see her father's mood shift immediately. It was the same sad look he had whenever he spoke of NERV or the war.

"Then we had to go in for the first Synch Test since the accident. Asuka and I didn't really want to go, but we had a duty to perform. And, honestly, it was something to take our mind off things for a bit. When we synched with the Eva, we had to clear our minds and focus solely on the connection. But the last time we had been in our entry plugs had been when the accident occurred. The results didn't make your mother very happy."

--

"WHAT DO YOU MEAN MY SCORE IS DOWN TEN POINTS?!"

Asuka was livid, his face having gone red in anger at even the possibility that he had dropped in performance. Shinji, Rei and Asuka were still all in their plug suits as Dr. Akagi reviewed the results of their synch test.

"Both you and Shinji have shown a ten point drop in your synch ratios. This was expected due to recent events. I believe it has to do with the altered biochemistry of your brains and altered physiology due to the change the nano-probes caused. This is only temporary and you should be back to normal ratios within the next few weeks of testing. Aside from that, nothing else has changed. You should both go home and rest. As far as I can determine you are both doing as well as can be expected," Ritsuko concluded her voice as businesslike as always.

"How long are we stuck like this?" Shinji asked timidly. The Third Child wanted to be back to normal as soon as possible.

"Right now we are growing a new batch of nano-probes. It's a very delicate operation and extremely slow. There have been problems with the growth rate and programming. We're hoping we can recreate the accident and have you both back to normal within another four months," Ritsuko answered.

Asuka just sucked it up and set himself towards his goal of reclaiming his lost synch points. In a way that was all he thought about; not even the change had stopped Asuka's endless pursuit of being the best. It was his obsession.

The Children were dismissed and allowed to remove their plug suits. Asuka went into the male locker room and got ready to disrobe as Shinji went into the female locker room. Asuka didn't really mind it too much; the male locker room was completely empty except for him. It gave him the privacy he had been missing since coming to Japan. Shinji on the other hand was horribly embarrassed having to change next to Rei.

Her insecurity had not been unnoticed by Rei, who found it rather puzzling. Ikari should not be uneasy around her, as she had previously seen her naked. And now that Ikari was also female the embarrassment was completely unfounded in her mind. Perhaps she would ask Commander Ikari to help her understand this.

Shinji just went about changing into her street clothes after Rei left.

When Shinji left the locker room, she found Asuka had been waiting for her. In fact Asuka had a rather irritated expression on his face. He stood there impatiently tapping his foot on the ground as Shinji walked towards him.

"Took you long enough. I was starting to think you were doing some perverted things to that body you've got now," Asuka said, however thinking about those "perverted things" came back to haunt the Second Child.

"DAMNIT! Why can't I keep this thing under control?!" He screamed as "Little Asuka" decided that he was interested in something.

"It could be worse I suppose."

"Oh and how could it possibly get any worse then this, Third Child?!"

Just then, a loud siren began to resonate throughout the halls of NERV, and Asuka was about to find out just how bad 'bad' could get.

--

"Asuka, are you there yet?" Shinji asked. She had been the first in position and had sighted the angel. It sat in the sky like a black marble, streaked in white. Something was making the hair on the back of her neck stand up as she watched the Angel just float over Tokyo-3.

"Not yet. You know an Eva can't move that fast!" Asuka replied, his voice filled with annoyance.

Unit-02 moved slowly through the city, keeping cover behind the taller munitions buildings and power stations. He had just finished switching plugs when he heard Shinji's voice cry out for help.

"AT field detected! Pattern Blue! IT'S RIGHT BENEATH UNIT-01!"

The shadow had covered the street under Unit-01's feet suddenly, that was when it began. Shinji could feel the Eva beginning to sink into the inky black the Angel had created. Fear had engulfed Shinji's mind as she tried to break free, but her legs wouldn't move. Unit-01 was stuck, and going further down.

By the time Asuka and Rei had gotten to a point they could help, it was all over.

--

_I can't believe she got herself into this mess, _Asuka fumed. But that wasn't the only thing pissing him off. It wasn't even the biggest thing on his mind. What was had been his failure.

His failure to save Shinji from what had happened. That had struck Asuka rather suddenly, but as he thought of it it made sense really. He wanted to be the best Eva pilot, that meant more then simply high synch ratios and skill. It meant actually performing better then his competition.

And Shinji still had the better kill record. That was annoying as all Hell, that Shinji could have killed as many Angels without the level of training Asuka had. Ever since the war had begun Shinji had been in the lead. Even before Asuka had been given a shot, Shinji had outperformed him. Now, through no fault of her own, Shinji had been sucked into the abyss. Asuka thought on that as the plans were laid, time tables set. Being the best didn't just mean you were the best out of everyone, it meant you became the target of anyone who wanted to take your spot. It also meant being the target of your enemies first off when the best is usually the greatest threat to them.

Now they had called everyone into the briefing area, Rei had already joined them and Asuka was now standing in the back listening. To Asuka's shock, they had not planned on rescuing Unit-01's pilot at all.

--

Shinji sat in her entry plug. It had been so long since she had been forced to go to to minimal systems in order to survive. For all she knew she would die there. Cold, alone, and for some reason hungry. It seemed out of all the problems Shinji had right now that food being in the top three was in some way a sick joke at her expense. It didn't make sense, none of this did.

All Shinji could do was to try to sleep and conserve some of her precious life support that remained. Even if there was no hope of rescue or survival, she could last a while longer. At least it would be a quiet death, as he body slowly shut down from oxygen deprivation as the LCL went beyond the point the recyclers could handle.

Slowly, Shinji slipped into a restless sleep. As she did she felt as if for a moment she were simply at peace with the world around her. She did not think of anything that would be coming for her, even death. As she slept her mind slipped somewhere.

Shinji was on the train now, speeding around Tokyo-3. She was just looking out the window, watching the great city as she passed. As Shinji turned her head she saw something odd. Whenever Shinji had had these flashes before she had been confronted by the child she had been, this time however.

Standing before her with his hands in his pockets was the boy she had been. His attitude and everything was still the same as it had been, shy and unassuming. However this version seemed a bit more sure of the situation. She wasn't surprised, he always was, no matter what form he took. Even as a small child this specter seemed to always know more then she did.

"You still see yourself as you were before," the other Shinji said.

"Yes, it's who I am," Shinji answered.

"Who you are isn't bound by what you look like. You are who you are, no more, no less," the Other said.

"What does that mean!"

"It means you should accept the reality of your existence," the doppleganger said.

"That is not easy," Shinji said, her voice.

The odd child simply smiled, "It never is."

--

"I never quiet remembered what happened inside that place. There was nothing, no sound, no up, no down, only unending white light. The next thing I really remember was waking up in NERV Medical yet again," Shinji said as he sipped his tea.

Yui smiled as her father spoke. She had heard much of the war from both her parents, their friends and family. But the way her father spoke now was as if she was hearing it for the first time. Perhaps it was because of what she knew now, or perhaps it was because he wasn't trying to edit himself to ignore that part he'd hidden forever.

She looked at her watch and groaned, it was starting to get late in the day and her husband would be at home worried about her soon. Shinji noticed and smiled, "It's getting late, why don't you go on home for the night. I'll tell you more tomorrow."

Yui smiled and got up with some difficulty. Her father took her hand to help her then pulled her into a light hug. "You take care Yui, I'll see you tomorrow."

Yui left, and as she walked to the elevator Shinji couldn't help but wonder if he was doing the right thing telling her all this. He shook his head, she had a right to know where she came from. Shinji also realized he had a more selfish reason for telling her.

He could no longer hide this from her, anyone else but her.

To Be Continued...

Next Chapter: The Angels keep coming, disregarding the trials of man. Shinji and Asuka slowly come to terms with what has happened with them. And the Fourth Child will be given his chance to take on part of the burden his friends have been forced to carry on their own.

Next Chapter: Thirteen O'Clock


End file.
